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                                           *** TEXT OMITTED AND FILED SEPARATELY
                                                CONFIDENTIAL TREATMENT REQUESTED

                                                                   EXHIBIT 10.31

                             FIRST AMENDMENT OF THE
                             COLLABORATION AGREEMENT

         This First Amendment (this "FIRST AMENDMENT") to the Collaboration
Agreement is made and entered into as of October 16, 2002 by and between
EPIMMUNE INC., having a principal place of business at 5820 Nancy Ridge Drive,
San Diego, CA 92121 ("EPMN"), and GENENCOR INTERNATIONAL, INC., having a
principal place of business at 925 Page Mill Road, Palo Alto, CA 94304-1013
("GCOR") (collectively referred to herein as the "PARTIES") agree as follows:

         WHEREAS, the Parties have entered into that certain Collaboration
Agreement dated July 9, 2001 (the "COLLABORATION AGREEMENT"); and

         WHEREAS, the Parties wish to amend the Collaboration Agreement on the
terms and conditions set forth herein;

         NOW, THEREFORE, in consideration of the mutual undertakings of the
Parties as set forth below as well as other good and valuable consideration, the
receipt and sufficiency of which is hereby acknowledged, GCOR and EPMN do hereby
mutually agree as follows:

A. With respect to funding during the Extended Term (as defined below), Section
4.1 shall be amended to add subsection (b) as follows:

4.1  (a) Funding. Subject to the terms and conditions set forth herein, during
     the Collaboration Term GCOR shall fund annually up to [...***...] EPMN
     FTE's at [...***...] for the work performed under the Work Plan. This
     payment is based on the [...***...] expended by EPMN in support of the
     Program.

     (b) Funding - Extended Term. Subject to the terms and conditions set forth
     herein, during the Extended Term GCOR shall fund annually between
     [...***...] EPMN FTE's at [...***...] for the work performed under the Work
     Plan. This payment is based on the [...***...] expended by EPMN in support
     of the Program.

B.   With respect to the term of Collaboration Agreement and termination
     thereof, Sections 8.1 and 8.4 shall be amended to read as follows:

8.1 (a)  Term. This Agreement, unless terminated sooner as provided elsewhere
         herein, shall expire on September 1, 2004, which term can be extended
         by mutual agreement of the Parties.

    (b)  Extended Term. Between September 1, 2003 and September 1, 2004, GCOR
         may terminate this Agreement at any time, by providing three months
         prior written notice.

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                                              * CONFIDENTIAL TREATMENT REQUESTED

8.4  Effect of Termination by GCOR. In the event of termination by GCOR pursuant
     to Sections 8.1, 8.2 or 8.3, GCOR shall pay to EPMN all payments for
     [...***...] actually expended by EPMN as of the effective date of
     termination but shall have no further obligation to make payment for work
     that was not performed as of the effective date of termination. GCOR may as
     its discretion and cost, ask EPMN to continue to work on the Program for no
     more than [...***...] in order to wind down all research and development
     efforts. Upon such termination, EPMN shall promptly provide the Final
     Report of Section 2.7 to GCOR. In the event of such termination, the
     provisions of Section 10.5.3 of the License Agreement shall apply.

C.   All terms and conditions of the Collaboration Agreement remain in full
     force and effect, as modified hereby and are hereby ratified by the
     parties.

D.   From and after the effective date of this First Amendment to the
     Collaboration Agreement, the term "Agreement" shall be deemed to mean the
     Collaboration Agreement as hereby modified.

         IN WITNESS WHEREOF, the Parties have caused this First Amendment to the
Collaboration Agreement to be executed by and through their duly authorized
representatives as of the date first above written.

EPIMMUNE INC.

By: /s/ Robert J. De Vaere
    -----------------------------
    Robert J. De Vaere
    Vice President, Finance and
    Chief Financial Officer

GENENCOR INTERNATIONAL, INC.

By: /s/ Debby Jo Blank
    -----------------------------
    Debby Jo Blank

Title: Senior Vice President, Healthcare

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